Jan. 27th 2015

  • Goal : To identify baseline DNA methylation markers that predict the change in PHQ (Aim 1)

  • Model : PHQchange = a + b * BaselineMethylation + e

  • Sites : 437247

  • Sample size: 65

  • Multiple Testing Correction : Bonferroni

  • 5% MinP Cutoff - Raw PHQchange :

  • 5% MinP Cutoff - INV PHQchange :

Association Test

Raw PHQchange ~ Baseline Methylation

QQplot of pvals based on Raw PHQchange and CI

Results based on Raw PHQchange
CpG Chr Genes Pos beta pval p.adj size
cg25660390 17 NA 73073700 0.003 0.0e+00 0.0039 65
cg07219643 12 WSB2 118499016 0.001 1.0e-07 0.0327 65
cg15286044 10 CRTAC1 99789971 0.004 1.0e-07 0.0381 65
cg23932859 5 MEGF10 126625777 0.008 2.0e-07 0.0989 65
cg23679073 2 ZC3H15 187350909 0.002 3.0e-07 0.1408 65
cg26752884 11 JRKL;CCDC82 96123217 0.002 4.0e-07 0.1802 65
cg04992638 17 LOC100133991;C17orf46 43339328 0.002 4.0e-07 0.1889 65
cg25365565 6 HIST1H2BJ;HIST1H2AG 27101050 0.001 1.0e-06 0.4479 65
cg24190377 17 C17orf101 80350294 -0.001 1.1e-06 0.4659 65
cg22327690 17 TRIM37 57179774 -0.004 1.4e-06 0.6174 65

Studentized Residual QQ plots top 6 sites - raw PHQchange

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63127 
   65 

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63127 
   65 

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63127 
   65 

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50136 
   65 

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63127 
   65 

[[6]]
63127 
   65

Leverage Plots top 6 sites - raw PHQchange

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Cook's Distance - raw PHQchange

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PCA on top sites - Scree Plot

PCA on top sites - biplot

Association Test

INV PHQchange ~ Baseline Methylation

QQplot of pvals based on INV PHQchange and CI

QQplot: adj by covariates

QQplot: all sites 437247 vs thinned 106586

QQplot and CI: thinned sites 106586

QQplot and CI: thinned sites 106586

Results based on INV PHQchange
CpG Chr Genes Pos beta pval p.adj size
cg07219643 12 WSB2 118499016 0.004 1.0e-07 0.0510 65
cg23679073 2 ZC3H15 187350909 0.008 1.0e-07 0.0575 65
cg15286044 10 CRTAC1 99789971 0.013 7.0e-07 0.2946 65
cg00220389 17 NA 80455521 0.006 7.0e-07 0.3118 65
cg07696033 11 ALX4 44326410 0.008 1.1e-06 0.4659 65
cg20696752 17 LSM12 42143797 0.004 1.5e-06 0.6718 65
cg14613271 2 SLC5A7 108602931 0.013 2.2e-06 0.9507 65
cg02592615 6 HIVEP1 12012261 0.010 2.5e-06 1.0000 65
cg07399094 6 NA 3163461 0.007 2.9e-06 1.0000 65
cg26752884 11 JRKL;CCDC82 96123217 0.006 3.0e-06 1.0000 65

Residual QQ plots top 6 sites - INV PHQchange

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63127 
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63127 
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63127 
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63127 
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63127 
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63127 
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Leverage Plots top 6 sites - INV PHQchange

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Cook's Distance - INV PHQchange

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PCA on top sites - Scree Plot

PCA on top sites - biplot

Association Test

INV PHQchange ~ INV Baseline Methylation

QQplot pvals : INV PHQchange ~ INV Base Methylation

ScatterPlot: -log10 InvDiffMethyl vs -log10 DiffMethyl

Results based on INV PHQchange ~ INV Base Methylation
CpG Chr Genes Pos beta pval p.adj size
cg23679073 2 ZC3H15 187350909 0.602 1.0e-07 0.0496 65
cg07219643 12 WSB2 118499016 0.586 3.0e-07 0.1312 65
cg15286044 10 CRTAC1 99789971 0.571 7.0e-07 0.3004 65
cg26880187 12 ERBB3 56473976 0.568 8.0e-07 0.3505 65
cg00220389 17 NA 80455521 0.568 8.0e-07 0.3573 65
cg02592615 6 HIVEP1 12012261 0.565 1.0e-06 0.4264 65
cg25429640 5 UNC5A 176302913 0.560 1.3e-06 0.5539 65
cg02370807 5 HNRNPAB 177632259 0.560 1.3e-06 0.5593 65
cg07696033 11 ALX4 44326410 0.557 1.5e-06 0.6386 65
cg26752884 11 JRKL;CCDC82 96123217 0.554 1.7e-06 0.7632 65

Residual QQ plots top 6 sites

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63127 
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54075 
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50136 
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50136 
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63127 
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Leverage Plots top 6 sites

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Cook's Distance : INV PHQchange ~ INV Base Methylation

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PCA on top sites - Scree Plot

PCA on top sites - biplot